Systems biology at its best tightly couples experimental biology with modeling methodologies. Experimental later keep the theories generated through computation realistic; carefully constructed mathematical models 'can generate new testable hypotheses. Achieving this balance, however, demands interdisciplinary collaborations such as set up in the CHAIN Center, and the experience and skills as available in this Core. The Systems Biology and Integrative Networks Core (SB-INC, aka Systems Biology Core) is to enable genome-scale technology and state-of-the-art bioinformatics tools for the study of neuroAIDS. CHAIN researchers can to collect or analyze genome-scale data though active collaboration with members of the SB-INC Available experimental platforms include RNA-seq, chlP-seq, and protein interaction screens via Y2H and M2H. Available bioinformatic technologies include clustering and classification of gene expression or metabolomic profiles, integration of molecular profiles with molecular networks, and identification of network-based biomarkers. SB-INC will also support research and development centered on combinatorial transcriptional interaction maps. We will map the transcripfional networks underlying developmental processes of high relevance to neuroAIDS, including neuronal degeneration and protection and activation and differentiation of macrophages. Through these methods we will develop network-based biomarkers to predict the potential for development of neuroAIDS, the presence of neuroAIDS, and response to treatment.